Table of Contents

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3D Atlas rendering plugin

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User Manual

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Introduction

The 3D Atlas rendering plugin allows the user to view and manipulate digital atlases in the three orthogonal planar views. The user can interactively select the plane coordinates of any of the orthogonal views, show/hide labels of the atlas, and view a graph of the atlas hierarchy.

Getting Started

To open a file using the 3D atlas rendering plugin

1. Open the Viewer Workspace.
2. If in DualView mode, select the target Viewport (Left-mouse-click anywhere in the viewport in the data display area).
3. In the Layer Controls, open the dropdown menu to the right of the Open File button.
4. Select 3D atlas. An open file dialog box appears. Navigate to and select the file(s) you want to open (multiple selection allowed using Shift+Left-mouse-click). Click Open. If successful, the digital atlas (volume with colored labels) will appear in the data display area and the label hierarchy graphs will intially be docked to the left-side of the main application frame.

File Formats supported

• .atlas file (Specification)

Cart objects supported

1. none

User interface

• GUI controls
  • Show/Hide: button to show/hide the layer in the viewport
  • Opacity: slider/spinner to adjust the opacity of the layer
  • Image(s): slider/spinner to cine through multiple images of the current axis
  • Contrast: slider/spinner to adjust the image contrast
  • Brightness: slider/spinner to adjust the image brightness
  • Axis: radiobutton group to select the current axis to view
  • Flip: buttons to flip the images in the X,Y,and Z axes
  • Expand/Collapse: button to expand/collapse the GUI controls
  • Label Opacity: slider/spinner to adjust the opacity of the label colors
  • Label Set: combobox to select the active label hierarchy (for multiple labels when applicable)

• Keyboard controls
  • Left/Right Arrows: Previous/Next image
  • Up/Down Arrows: Opacity Increase/Decrease

• HUD Thumbnails
  • When a 3D Atlas layer is selected, a heads-up-display (HUD) is overlayed in the viewport that shows the three orthogonal view thumbnails for the currently selected planes. Left-mouse-click and drag inside any of the orthogonal thumbnail views will change the currently selected plane to view.

• Status Bar: When the layer is selected, a status bar is displayed on the bottom of the viewport that shows:
  • Name of the layer (top-left)
  • Image dimensions of the current axis (top-right)
  • Image coordinates relative to the bottom left corner of the current image (bottom-left)
  • Current slice number for each dimension (bottom-right)

• Display scale
  • When the layer is selected, the scale measurements in real physical dimensions are overlayed in the upper right hand corner of the current viewport.

• Atlas UI (applied to the layer in the viewport)
  • Mouse left-double-click: select/deselect the label under the mouse cursor. For atlases with multiple hierarchies, the corresponding label for the other labels are also selected/deselected.
  • Shift + Mouse left-double-click: group select labels
  • Mouse hover: moving the mouse cursor over a label in the 3D atlas layer will display the name of the label on the screen. When multiple label hierarchies are available, the corresponding labels are also shown below the primary label.
  • Mouse right-double-click: if labels have been selected, switches to the Search workspace and sends the name of the labels to the keyword search

• Graph UI
  • see the Graph Manager

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Functional Specification

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Data input methods

Input Method	Supported	Notes
loading from file	yes
loading from the cart	no
adding a layer	no

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Serializing/deserializing

In the serialization process, following states are saved:

• Rotation
• Scaling
• Translation
• Brightness
• Contrast
• Opacity
• Label opacity
• Active axis (Transverse/Sagittal/Horizontal)
• Active image number
• X-Flip, Y-Flip and Z-Flip values.

Deserialization process restores all the above states.

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Linking

• 3D Atlas - 3D Atlas: using the GUI controls, keyboard controls, and HUD thumbnail controls in the master layer will change all the corresponding controls in the slave layers.
  • Image(s): slave layer is set to proportional image number of master layer (ie: if master layer image is set to 50 of 100 then slave layer is set to image 2 of 4)
  • Label Set: ignored for slave layers
  • Atlas UI: ignored for slave layers
• 3D Atlas - 2D Image:
  3D Atlas - 3D Volume:
  • Opacity, Contrast, Brightness, Axis, Flip: mirrors master layer changes
  • Image(s): slave layer is set to proportional image number of master layer (ie: if master layer image is set to 50 of 100 then slave layer is set to image 2 of 4)

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Workspace Interoperability

None

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Error Handling

Method	Object	Error	Exception thrown	Notes
load()	File	file not found	yes	java.io.FileNotFoundException
		bad file extension	yes	java.io.IOException
		xml error	yes	java.lang.Exception

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DarenLee^? - 27 Apr 2009